Update ver 0.4.1

README.md

@@ -16,6 +16,10 @@ If you want to use developmental version, it can be installed using the followin
 `pip install git+https://github.com/ponnhide/patchworklib.git`
 
 ## News
+#### 04182022: Version 0.4.1 is released. 
+- `load_seaborngrid` can accepts a `seaborn.clustermap` plot. For details, see example code on [Google colab](https://colab.research.google.com/drive/1wQQyBHLNXJ5Ks6ev88IjXhGfT98SGJuM?usp=sharing)
+- Some bugs were fixed.
+
 #### 03272022: Version 0.4.0 is released. 
 - Add docstring for each method and class 
 - Add some new methods of `patchworklib.Bricks` class to set common label, title, spine and colorbar for `Brick` objets in the `Bricks` object. 

example/sup_elements.ipynb

@@ -127,7 +127,7 @@
  {
  "data": {
  "text/plain": [
- "<matplotlib.spines.Spine at 0x12231eac0>"
+ "<matplotlib.spines.Spine at 0x148651310>"
  ]
  },
  "execution_count": 5,
@@ -195,7 +195,7 @@
  ],
  "metadata": {
  "kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
  "language": "python",
  "name": "python3"
  },
@@ -209,7 +209,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.9.6"
+ "version": "3.9.9"
  }
  },
  "nbformat": 4,

patchworklib/modified_grid.py

@@ -3,11 +3,14 @@
 import pandas as pd
 import matplotlib as mpl
 import matplotlib.pyplot as plt
+from matplotlib import gridspec
 from itertools import product
 
 import seaborn 
 from inspect import signature
 from seaborn.axisgrid import FacetGrid, JointGrid, PairGrid, Grid 
+import seaborn.matrix as sm
+from seaborn.matrix import ClusterGrid
 from seaborn._core import VectorPlotter, variable_type, categorical_order
 from seaborn import utils
 from seaborn.utils import _check_argument, adjust_legend_subtitles, _draw_figure
@@ -461,3 +464,114 @@ def __setattr_for_clustergrid__(self, key, value):
  else:
  super.__setattr__(self, key, value)
 
+def __init_for_clustergrid__(self, data, pivot_kws=None, z_score=None, standard_scale=None,
+ figsize=None, row_colors=None, col_colors=None, mask=None,
+ dendrogram_ratio=None, colors_ratio=None, cbar_pos=None):
+ """Grid object for organizing clustered heatmap input on to axes"""
+ try:
+ import scipy
+ except:
+ raise RuntimeError("ClusterGrid requires scipy to be available")
+
+ if isinstance(data, pd.DataFrame):
+ self.data = data
+ else:
+ self.data = pd.DataFrame(data)
+
+ self.data2d = self.format_data(self.data, pivot_kws, z_score,
+ standard_scale)
+
+ self.mask = sm._matrix_mask(self.data2d, mask)
+
+ self._figure = Grid._figure #Modified by Hideto
+ self._figsize = figsize
+ self._figure.set_size_inches(figsize)
+ #self._figure = plt.figure(figsize=figsize)
+
+ self.row_colors, self.row_color_labels = \
+ self._preprocess_colors(data, row_colors, axis=0)
+ self.col_colors, self.col_color_labels = \
+ self._preprocess_colors(data, col_colors, axis=1)
+
+ try:
+ row_dendrogram_ratio, col_dendrogram_ratio = dendrogram_ratio
+ except TypeError:
+ row_dendrogram_ratio = col_dendrogram_ratio = dendrogram_ratio
+
+ try:
+ row_colors_ratio, col_colors_ratio = colors_ratio
+ except TypeError:
+ row_colors_ratio = col_colors_ratio = colors_ratio
+
+ width_ratios = self.dim_ratios(self.row_colors,
+ row_dendrogram_ratio,
+ row_colors_ratio)
+ height_ratios = self.dim_ratios(self.col_colors,
+ col_dendrogram_ratio,
+ col_colors_ratio)
+
+ nrows = 2 if self.col_colors is None else 3
+ ncols = 2 if self.row_colors is None else 3
+
+ self.gs = gridspec.GridSpec(nrows, ncols,
+ width_ratios=width_ratios,
+ height_ratios=height_ratios, wspace=0, hspace=0)
+
+ self.ax_row_dendrogram = self._figure.add_subplot(self.gs[-1, 0])
+ self.ax_col_dendrogram = self._figure.add_subplot(self.gs[0, -1])
+ self.ax_row_dendrogram.set_axis_off()
+ self.ax_col_dendrogram.set_axis_off()
+
+ self.ax_row_colors = None
+ self.ax_col_colors = None
+
+ if self.row_colors is not None:
+ self.ax_row_colors = self._figure.add_subplot(
+ self.gs[-1, 1])
+ if self.col_colors is not None:
+ self.ax_col_colors = self._figure.add_subplot(
+ self.gs[1, -1])
+
+ self.ax_heatmap = self._figure.add_subplot(self.gs[-1, -1])
+ if cbar_pos is None:
+ self.ax_cbar = self.cax = None
+ else:
+ # Initialize the colorbar axes in the gridspec so that tight_layout
+ # works. We will move it where it belongs later. This is a hack.
+ self.ax_cbar = self._figure.add_subplot(self.gs[0, 0])
+ self.cax = self.ax_cbar # Backwards compatibility
+ self.cbar_pos = cbar_pos
+
+ self.dendrogram_row = None
+ self.dendrogram_col = None
+
+def __plot_for_clustergrid__(self, metric, method, colorbar_kws, row_cluster, col_cluster, row_linkage, col_linkage, tree_kws, **kws):
+ # heatmap square=True sets the aspect ratio on the axes, but that is
+ # not compatible with the multi-axes layout of clustergrid
+ if kws.get("square", False):
+ msg = "``square=True`` ignored in clustermap"
+ warnings.warn(msg)
+ kws.pop("square")
+
+ colorbar_kws = {} if colorbar_kws is None else colorbar_kws
+
+ self.plot_dendrograms(row_cluster, col_cluster, metric, method,
+ row_linkage=row_linkage, col_linkage=col_linkage,
+ tree_kws=tree_kws)
+
+ try:
+ xind = self.dendrogram_col.reordered_ind
+ except AttributeError:
+ xind = np.arange(self.data2d.shape[1])
+
+ try:
+ yind = self.dendrogram_row.reordered_ind
+ except AttributeError:
+ yind = np.arange(self.data2d.shape[0])
+
+ self.plot_colors(xind, yind, **kws)
+ self.plot_matrix(colorbar_kws, xind, yind, **kws)
+ self._figure.set_size_inches((1,1))
+ #mpl.rcParams["figure.subplot.hspace"] = hspace 
+ #mpl.rcParams["figure.subplot.wspace"] = wspace
+ return self